Yes, you can do that, and countries do. Ships will burn cleaner fuels when they are in territorial waters for this reason. The problem is they're still doing environmental damage out in international waters.

What you need to do is put the foot down and prevent flags of convenience (or more specifically, those that fail to meet environmental standards) from docking at your ports at all. Which I'm not sure is permissible under maritime laws.

(or maybe there is some dodge like preventing the ship from "carrying hazmat" which you define as bunker fuel, or ban ships from having soot in their stacks that has sulfur deposits, or so on...)